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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ), 'gf_id' => 'HOM05D001233', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001233' ), 'data_identifier' => 'HOM05D001233', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001233', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p06990' => 'bna', 'A03p32620' => 'bna', 'A03p65520' => 'bna', 'A05p26830' => 'bna', 'A05p31850' => 'bna', 'A10p23720' => 'bna', 'Aa31LG11G14420' => 'aar', 'Aa31LG4G16450' => 'aar', 'Aa31LG8G4810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3114' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5283' => 'aag', 'Actinidia02707' => 'ach', 'Actinidia34986' => 'ach', 'Actinidia35131' => 'ach', 'Ah.10g031440' => 'amhyb', 'Ah.11g050370' => 'amhyb', 'AL3G10980' => 'aly', 'AL3G31110' => 'aly', 'AL5G27090' => 'aly', 'AL6G25960' => 'aly', 'Aqoxy3G00714' => 'aox', 'Aqoxy3G03318' => 'aox', 'Aqoxy3G03320' => 'aox', 'Aqoxy3G04086' => 'aox', 'arahy.Tifrunner.gnm1.ann1.54ZV2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M2CKH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.95KH60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B84EEW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EPH7QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBB9ZN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7YHKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1NLX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQNW98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWA65T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y3RZ5Q' => 'arhy', 'AT3G01260' => 'ath', 'AT3G17940' => 'ath', 'AT3G47800' => 'ath', 'AT5G15140' => 'ath', 'ATR0564G286' => 'atr', 'ATR0564G317' => 'atr', 'Atru.chr1.1902' => 'acertr', 'Atru.chr3.100' => 'acertr', 'Atru.chr3.99' => 'acertr', 'Atru.chr8.2588' => 'acertr', 'Atru.chr8.2589' => 'acertr', 'Atru.chr8.2669' => 'acertr', 'Atru.chr8.2672' => 'acertr', 'Atru.chr8.2673' => 'acertr', 'Atru.chr9.1677' => 'acertr', 'Atru.chr9.1711' => 'acertr', 'Atru.chr9.2290' => 'acertr', 'AUR62011992' => 'cqu', 'AUR62018107' => 'cqu', 'AUR62031614' => 'cqu', 'AUR62032311' => 'cqu', 'AUR62038860' => 'cqu', 'BcaB01g00876' => 'bca', 'BcaB01g05078' => 'bca', 'BcaB04g20804' => 'bca', 'BcaB06g25862' => 'bca', 'BcaB08g36922' => 'bca', 'BcaB08g36924' => 'bca', 'BcaC01g01776' => 'bca', 'BcaC01g04418' => 'bca', 'BcaC01g04514' => 'bca', 'BcaC05g25886' => 'bca', 'BcaC05g27122' => 'bca', 'BcaC05g28731' => 'bca', 'BcaC08g43981' => 'bca', 'BcaC09g48757' => 'bca', 'BcaNung02012' => 'bca', 'BolC1t02500H' => 'bol', 'BolC1t04583H' => 'bol', 'BolC3t13294H' => 'bol', 'BolC3t16235H' => 'bol', 'BolC3t16305H' => 'bol', 'BolC3t19497H' => 'bol', 'BolC5t30551H' => 'bol', 'BolC5t31741H' => 'bol', 'BolC5t33568H' => 'bol', 'BolC6t36560H' => 'bol', 'BolC7t44841H' => 'bol', 'BolC9t59038H' => 'bol', 'BraA01t03710Z' => 'bra', 'BraA03t10020Z' => 'bra', 'BraA03t12430Z' => 'bra', 'BraA04t16775Z' => 'bra', 'BraA05t21561Z' => 'bra', 'BraA05t21562Z' => 'bra', 'BraA05t22017Z' => 'bra', 'BraA06t25068Z' => 'bra', 'BraA10t44434Z' => 'bra', 'C01p25490' => 'bna', 'C01p46220' => 'bna', 'C03p07970' => 'bna', 'C03p39710' => 'bna', 'C03p40400' => 'bna', 'C03p71990' => 'bna', 'C05p18420' => 'bna', 'C05p30050' => 'bna', 'C05p48340' => 'bna', 'C06p13840' => 'bna', 'C07p43150' => 'bna', 'C09p61990' => 'bna', 'CAN.G1305.6' => 'can', 'CAN.G206.128' => 'can', 'CAN.G206.129' => 'can', 'CAN.G206.130' => 'can', 'CAN.G206.131' => 'can', 'CAN.G206.132' => 'can', 'CAN.G206.133' => 'can', 'CAN.G206.134' => 'can', 'CAN.G843.51' => 'can', 'CANSAT64G0969' => 'cansat', 'CANSAT64G2092' => 'cansat', 'CANSAT64G2877' => 'cansat', 'CANSAT80G1969' => 'cansat', 'CARHR075780' => 'chi', 'CARHR093270' => 'chi', 'CARHR156480' => 'chi', 'CARHR198170' => 'chi', 'Carub.0003s1767' => 'cru', 'Carub.0005s1391' => 'cru', 'Carub.0006s1331' => 'cru', 'Ca_03967_v3' => 'car', 'Ca_25337_v3' => 'car', 'Ca_29639_v3' => 'car', 'CBR_g49415' => 'cbr', 'Cc00_g05980' => 'ccan', 'Cc00_g06000' => 'ccan', 'Cc04_g06190' => 'ccan', 'Cc04_g17190' => 'ccan', 'Cc07_g03170' => 'ccan', 'Cc11_g04810' => 'ccan', 'CDE05G0622' => 'cde', 'CDE05G2233' => 'cde', 'Cfa007525' => 'cfa', 'Cfa018970' => 'cfa', 'Cfa024465' => 'cfa', 'Ciclev10008981m.g' => 'ccl', 'Ciclev10011989m.g' => 'ccl', 'Ciclev10012004m.g' => 'ccl', 'Ciclev10012137m.g' => 'ccl', 'Ciclev10024457m.g' => 'ccl', 'CiPaw.03G029100' => 'cil', 'CiPaw.11G041400' => 'cil', 'CiPaw.15G143900' => 'cil', 'ClCG06G005910' => 'cla', 'ClCG06G005920' => 'cla', 'ClCG06G014260' => 'cla', 'ClCG06G016310' => 'cla', 'ClCG10G014930' => 'cla', 'COL.COLO4_04911' => 'col', 'COL.COLO4_10426' => 'col', 'COL.COLO4_14036' => 'col', 'COL.COLO4_28295' => 'col', 'COL.COLO4_32769' => 'col', 'COL.COLO4_36109' => 'col', 'COL.COLO4_36110' => 'col', 'COL.COLO4_36111' => 'col', 'Cpa.g.sc14.24' => 'cpa', 'Cpa.g.sc14.25' => 'cpa', 'Cpa.g.sc3.391' => 'cpa', 'Cpa.g.sc388.4' => 'cpa', 'Cre06.g262050' => 'cre', 'CsaV3_1G002220' => 'csa', 'CsaV3_1G004410' => 'csa', 'CsaV3_3G041600' => 'csa', 'CsaV3_6G015090' => 'csa', 'CSS0006371' => 'camsi', 'CSS0013197' => 'camsi', 'CSS0015640' => 'camsi', 'CSS0019435' => 'camsi', 'CSS0025683' => 'camsi', 'CSS0029153' => 'camsi', 'CSS0029878' => 'camsi', 'DCAR_006723' => 'dca', 'DCAR_026067' => 'dca', 'DCAR_026068' => 'dca', 'DCAR_028347' => 'dca', 'Dinv06525' => 'din', 'Dinv08204' => 'din', 'Dinv19034' => 'din', 'Dinv19931' => 'din', 'Duzib084G0186' => 'dzi', 'Duzib147G0258' => 'dzi', 'Duzib147G0746' => 'dzi', 'Duzib205G0743' => 'dzi', 'ECA232G1282' => 'eca', 'ECA232G4212' => 'eca', 'ECA238G3057' => 'eca', 'EL10Ac2g02950' => 'bvu', 'EL10Ac5g10524' => 'bvu', 'Eucgr.B00459' => 'egr', 'Eucgr.B00816' => 'egr', 'Eucgr.B00995' => 'egr', 'Eucgr.J01219' => 'egr', 'FAN04G0147' => 'fan', 'FAN04G1457' => 'fan', 'FAN07G0729' => 'fan', 'FAN08G3202' => 'fan', 'FAN12G4119' => 'fan', 'FAN12G4301' => 'fan', 'FAN13G0800' => 'fan', 'FAN13G1865' => 'fan', 'FAN14G4863' => 'fan', 'FAN14G5228' => 'fan', 'FAN17G2376' => 'fan', 'FAN18G3927' => 'fan', 'FAN22G2076' => 'fan', 'FvH4_5g15261' => 'fve', 'FvH4_5g17440' => 'fve', 'FvH4_6g49081' => 'fve', 'Glyma.04G172800' => 'gma', 'Glyma.05G028400' => 'gma', 'Glyma.06G191500' => 'gma', 'Glyma.07G102900' => 'gma', 'Glyma.09G174902' => 'gma', 'Glyma.09G239800' => 'gma', 'Glyma.13G064200' => 'gma', 'Glyma.17G098400' => 'gma', 'Glyma.18G257700' => 'gma', 'Glyma.19G020700' => 'gma', 'Glyma.U031515' => 'gma', 'Gohir.A03G092700' => 'ghi', 'Gohir.A05G364600' => 'ghi', 'Gohir.A09G020000' => 'ghi', 'Gohir.A11G029801' => 'ghi', 'Gohir.D02G121600' => 'ghi', 'Gohir.D04G050200' => 'ghi', 'Gohir.D09G019600' => 'ghi', 'Gohir.D11G033200' => 'ghi', 'Gorai.005G132500' => 'gra', 'Gorai.006G023000' => 'gra', 'Gorai.007G036000' => 'gra', 'Gorai.012G055600' => 'gra', 'GSVIVG01008039001' => 'vvi', 'GSVIVG01008450001' => 'vvi', 'GSVIVG01011365001' => 'vvi', 'GSVIVG01011370001' => 'vvi', 'HanXRQChr09g0265471' => 'han', 'HanXRQChr14g0433261' => 'han', 'HanXRQChr15g0487791' => 'han', 'Haze_07354' => 'cav', 'Haze_14560' => 'cav', 'Haze_18873' => 'cav', 'Hma1.2p1_0158F.1_g070220' => 'hma', 'Hma1.2p1_0163F.1_g073070' => 'hma', 'Hma1.2p1_0449F.1_g155290' => 'hma', 'HPP92_006016' => 'vpl', 'HPP92_006017' => 'vpl', 'HPP92_010104' => 'vpl', 'HPP92_016460' => 'vpl', 'HPP92_027149' => 'vpl', 'Hund02844' => 'sun', 'Hund09517' => 'sun', 'Hund13230' => 'sun', 'Lalb_Chr02g0159601' => 'lal', 'Lalb_Chr08g0235901' => 'lal', 'Lalb_Chr12g0196791' => 'lal', 'Lalb_Chr14g0370601' => 'lal', 'Lalb_Chr24g0398161' => 'lal', 'Lj1g0004969' => 'lja', 'Lj1g0007234' => 'lja', 'Lj2g0002731' => 'lja', 'Lj2g0003443' => 'lja', 'Lj2g0019347' => 'lja', 'Lj5A158T78' => 'lonja', 'Lj7A399T58' => 'lonja', 'Lj7A442T85' => 'lonja', 'Lj7P398T62' => 'lonja', 'Lj9C460G7' => 'lonja', 'Lj9C476G16' => 'lonja', 'Lju41A24T35' => 'lonja', 'Lju41A24T37' => 'lonja', 'Lsat_1_v5_gn_2_11861' => 'lsa', 'Lsat_1_v5_gn_4_177060' => 'lsa', 'Manes.01G118100' => 'mes', 'Manes.06G095000' => 'mes', 'Manes.14G171800' => 'mes', 'Manes.15G176900' => 'mes', 'Manes.17G023300' => 'mes', 'Mapoly0058s0080' => 'mpo', 'MBI02_g10679_MAGBIO' => 'mbi', 'MBI02_g14423_MAGBIO' => 'mbi', 'MBI05_g00396_MAGBIO' => 'mbi', 'MBI12_g36339_MAGBIO' => 'mbi', 'MBI19_g25544_MAGBIO' => 'mbi', 'MCO12G155' => 'mco', 'MD06G1189900' => 'mdo', 'MD06G1227800' => 'mdo', 'MD14G1196700' => 'mdo', 'MD14G1236900' => 'mdo', 'MD17G1048800' => 'mdo', 'Medtr4g108260' => 'mtr', 'Medtr6g011550' => 'mtr', 'Medtr6g011560' => 'mtr', 'Medtr6g069630' => 'mtr', 'Medtr7g009930' => 'mtr', 'MELO3C009884.2' => 'cme', 'MELO3C017161.2' => 'cme', 'MELO3C017162.2' => 'cme', 'MELO3C017363.2' => 'cme', 'MELO3C035180.2' => 'cme', 'Migut.D01501' => 'egut', 'Migut.H00902' => 'egut', 'Migut.I00151' => 'egut', 'Migut.I00271' => 'egut', 'Migut.O00772' => 'egut', 'MSTRG.23953' => 'ama', 'MSTRG.9307' => 'ama', 'Nitab4.5_0000564g0200' => 'nta', 'Nitab4.5_0000564g0240' => 'nta', 'Nitab4.5_0000564g0260' => 'nta', 'Nitab4.5_0000785g0080' => 'nta', 'Nitab4.5_0006635g0040' => 'nta', 'Nitab4.5_0010010g0010' => 'nta', 'Nitab4.5_0012026g0020' => 'nta', 'Nitab4.5_0013135g0020' => 'nta', 'Nn1g02326' => 'nnu', 'Nn3g17164' => 'nnu', 'Nn3g18297' => 'nnu', 'Nn4g23083' => 'nnu', 'Nn4g24259' => 'nnu', 'Oeu006486.1' => 'oeu', 'Oeu031765.1' => 'oeu', 'Oeu033296.1' => 'oeu', 'Oeu042353.1' => 'oeu', 'Oeu050708.1' => 'oeu', 'Oeu056266.1' => 'oeu', 'Oeu060787.1' => 'oeu', 'Oeu060928.1' => 'oeu', 'Oeu061238.1' => 'oeu', 'Oeu062090.2' => 'oeu', 'Oeu064170.1' => 'oeu', 'Os02g0575800' => 'osa', 'Os03g0381000' => 'osa', 'Os04g0458300' => 'osa', 'Os04g0458600' => 'osa', 'Os09g0108600' => 'osa', 'Os10g0155500' => 'osa', 'Peaxi162Scf00009g00221' => 'pax', 'Peaxi162Scf00129g00433' => 'pax', 'Peaxi162Scf00314g00323' => 'pax', 'PGR044G2496' => 'pgr', 'PGR083G0890' => 'pgr', 'PGR083G1970' => 'pgr', 'PGR083G2604' => 'pgr', 'PGSC0003DMG400001317' => 'stu', 'PGSC0003DMG400001318' => 'stu', 'PGSC0003DMG400005754' => 'stu', 'PGSC0003DMG400018084' => 'stu', 'PGSC0003DMG401001316' => 'stu', 'PGSC0003DMG402001316' => 'stu', 'PGSC0003DMG403001316' => 'stu', 'Phvul.003G191500' => 'pvu', 'Phvul.004G027000' => 'pvu', 'Phvul.004G150200' => 'pvu', 'Phvul.008G042600' => 'pvu', 'Potri.004G129700' => 'ptr', 'Potri.012G045875' => 'ptr', 'Potri.012G128800' => 'ptr', 'Potri.017G080000' => 'ptr', 'Potri.017G080100' => 'ptr', 'Potri.017G080200' => 'ptr', 'Potri.017G129300' => 'ptr', 'Pp3c10_12280' => 'ppa', 'PRCOL_00003625' => 'pco', 'Prupe.3G270200' => 'ppe', 'Prupe.5G188800' => 'ppe', 'Prupe.5G234200' => 'ppe', 'Psat1g030840' => 'psa', 'Psat1g075720' => 'psa', 'Psat3g196000' => 'psa', 'Psat4g052800' => 'psa', 'PSO541G6516' => 'pso', 'PSO591G0335' => 'pso', 'PSO591G0417' => 'pso', 'PSO675G6450' => 'pso', 'QL02p081175' => 'qlo', 'QL02p081190' => 'qlo', 'QL06p003735' => 'qlo', 'QL10p016156' => 'qlo', 'QL10p029836' => 'qlo', 'QL10p030255' => 'qlo', 'QL93p0043_0009' => 'qlo', 'RcHm_v2.0_Chr2g0168911' => 'rch', 'RcHm_v2.0_Chr7g0178251' => 'rch', 'RcHm_v2.0_Chr7g0180821' => 'rch', 'Rhsim06G0140000' => 'rsi', 'Rhsim08G0067600' => 'rsi', 'Rhsim08G0067700' => 'rsi', 'Rhsim08G0067800' => 'rsi', 'Rhsim08G0127100' => 'rsi', 'Rhsim12G0157700' => 'rsi', 'RhsimUnG0099200' => 'rsi', 'Sabra12G0032100' => 'sbr', 'Sabra12G0096700' => 'sbr', 'Sabra17G0071500' => 'sbr', 'Sabra17G0071600' => 'sbr', 'Sabra17G0071700' => 'sbr', 'Sabra17G0071900' => 'sbr', 'Sabra17G0107700' => 'sbr', 'SalBow1G4915' => 'sbo', 'SalBow1G7573' => 'sbo', 'SalBow5G0844' => 'sbo', 'SalBow5G0907' => 'sbo', 'SalBow5G1115' => 'sbo', 'Sc05g0001190' => 'sci', 'Sc14g0005970' => 'sci', 'Sed0003220' => 'sed', 'Sed0017673' => 'sed', 'Sed0023736' => 'sed', 'SEGI_02999' => 'sgi', 'SEGI_06084' => 'sgi', 'SEGI_22927' => 'sgi', 'SEGI_23037' => 'sgi', 'SEGI_29665' => 'sgi', 'SEGI_32342' => 'sgi', 'SEGI_33884' => 'sgi', 'SGA_v2.0_scaffold124G33647' => 'sas', 'SGA_v2.0_scaffold56G20039' => 'sas', 'SGA_v2.0_scaffold59G20671' => 'sas', 'SHI12532' => 'shi', 'SHI12533' => 'shi', 'SHI12534' => 'shi', 'SMO356G0488' => 'smo', 'SMO356G0551' => 'smo', 'Solyc02g087770.3' => 'sly', 'Solyc02g087780.3' => 'sly', 'Solyc02g087790.2' => 'sly', 'Solyc02g087800.3' => 'sly', 'Solyc02g087810.3' => 'sly', 'Solyc02g087820.1' => 'sly', 'Solyc03g113030.4' => 'sly', 'Solyc03g118650.3' => 'sly', 'Sopen02g032500' => 'spe', 'Sopen02g032510' => 'spe', 'Sopen02g032520' => 'spe', 'Sopen02g032530' => 'spe', 'Sopen02g032540' => 'spe', 'Sopen03g032110' => 'spe', 'Sopen03g037610' => 'spe', 'Sopen08g012510' => 'spe', 'Sp3g16070' => 'spa', 'Sp5g14160' => 'spa', 'Sp6g28930' => 'spa', 'TAR371G1185' => 'tar', 'TAR622G0290' => 'tar', 'TAR622G1286' => 'tar', 'TAR629G0043' => 'tar', 'TAR629G3063' => 'tar', 'TAR729G0001' => 'tar', 'THA.LOC104802419' => 'tha', 'THA.LOC104819435' => 'tha', 'THA.LOC104820346' => 'tha', 'THA.LOC104821439' => 'tha', 'Thecc.03G055200' => 'tca', 'Thecc.03G082100' => 'tca', 'Thecc.03G082300' => 'tca', 'Thecc.04G077500' => 'tca', 'Thecc.04G099900' => 'tca', 'Thhalv10010502m.g' => 'esa', 'Thhalv10013324m.g' => 'esa', 'Thhalv10021070m.g' => 'esa', 'TPR.G34727' => 'tpr', 'TPR.G39962' => 'tpr', 'TPR.G4256' => 'tpr', 'TPR.G4289' => 'tpr', 'TPR.G4343' => 'tpr', 'TPR.G837' => 'tpr', 'TPR.G838' => 'tpr', 'TPR.G839' => 'tpr', 'TPR.G8648' => 'tpr', 'TWI32G0663' => 'twi', 'TWI32G1208' => 'twi', 'TWI60G0099' => 'twi', 'TWI60G0967' => 'twi', 'TWI60G1513' => 'twi', 'unitig_27.g24922' => 'ugi', 'unitig_52.g17574' => 'ugi', 'unitig_62.g23559' => 'ugi', 'vmacro16559' => 'vma', 'vmacro17773' => 'vma', 'vmacro18157' => 'vma', 'vmacro18158' => 'vma', 'vmacro18204' => 'vma', 'vmacro18205' => 'vma', 'VMungo0464G0168' => 'vmu', 'VMungo0464G0879' => 'vmu', 'VMungo0464G1448' => 'vmu', 'VMungo1215G1019' => 'vmu', 'VMungo1309G0690' => 'vmu', 'VMungo1383G3015' => 'vmu', 'Zm00001eb018480' => 'zma', 'Zm00001eb064300' => 'zma', 'Zm00001eb080870' => 'zma', 'Zm00001eb080890' => 'zma', 'Zm00001eb080910' => 'zma', 'Zm00001eb089120' => 'zma', 'Zm00001eb219880' => 'zma', 'Zm00001eb244910' => 'zma', 'Zm00001eb424010' => 'zma' ) $gf_id = 'HOM05D001233' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001233' ) $data_identifier = 'HOM05D001233' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 11, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 12, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 8, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 7, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 8, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424010' $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